This question really hit home for me. I loved having a boy's nn as a kid and my friends all thought Frankie was so cool. As an adult it got really old and I got teased. I don't like my given name of Frances so never really used it. When I start college in the fall, I'll be going by a form of my name but more fresh and feminine. (Francine)
Having the opposite sex nn is ok when you're small. I would advise your sister's friend to keep the nn Ruby to family and friends. It's cute, but kids can be cruel. He will establish his own identity and nn for school friends etc. as he grows up.